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-rw-r--r--gnu/packages/simulation.scm490
1 files changed, 489 insertions, 1 deletions
diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm
index a5b661e34d..6144e236a7 100644
--- a/gnu/packages/simulation.scm
+++ b/gnu/packages/simulation.scm
@@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2017 Paul Garlick <pgarlick@tourbillion-technology.com>
+;;; Copyright © 2017, 2018 Paul Garlick <pgarlick@tourbillion-technology.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -18,10 +18,13 @@
(define-module (gnu packages simulation)
#:use-module (gnu packages)
+ #:use-module (gnu packages algebra)
#:use-module (gnu packages base)
#:use-module (gnu packages bash)
#:use-module (gnu packages bison)
#:use-module (gnu packages boost)
+ #:use-module (gnu packages check)
+ #:use-module (gnu packages cmake)
#:use-module (gnu packages compression)
#:use-module (gnu packages flex)
#:use-module (gnu packages gettext)
@@ -35,6 +38,8 @@
#:use-module (gnu packages mpi)
#:use-module (gnu packages multiprecision)
#:use-module (gnu packages ncurses)
+ #:use-module (gnu packages pkg-config)
+ #:use-module (gnu packages python)
#:use-module (gnu packages readline)
#:use-module (gnu packages tls)
#:use-module (gnu packages version-control)
@@ -42,7 +47,9 @@
#:use-module (gnu packages xorg)
#:use-module (guix download)
#:use-module (guix build utils)
+ #:use-module (guix build-system cmake)
#:use-module (guix build-system gnu)
+ #:use-module (guix build-system python)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix utils)
@@ -221,3 +228,484 @@ with gas/liquid interfaces. Large problems may be split into smaller, connected
problems for efficient solution on parallel systems.")
(license license:gpl3+)
(home-page "https://openfoam.org")))
+
+(define-public python-fenics-dijitso
+ (package
+ (name "python-fenics-dijitso")
+ (version "2018.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "fenics-dijitso" version))
+ (sha256
+ (base32
+ "1qax2f52qsjbd1h5lk5i5shp448qlakxabjjybrfc1w823p0yql9"))))
+ (build-system python-build-system)
+ (inputs
+ `(("openmpi" ,openmpi)
+ ("python-numpy" ,python-numpy)))
+ (native-inputs
+ `(("python-pytest-cov" ,python-pytest-cov)))
+ (propagated-inputs
+ `(("python-mpi4py" ,python-mpi4py)))
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'build 'mpi-setup
+ ,%openmpi-setup)
+ (replace 'check
+ (lambda _
+ (setenv "HOME" "/tmp")
+ (setenv "PYTHONPATH"
+ (string-append (getcwd) ":" (getenv "PYTHONPATH")))
+ (with-directory-excursion "test"
+ (invoke "./runtests.sh"))
+ #t)))))
+ (home-page "https://bitbucket.org/fenics-project/dijitso/")
+ (synopsis "Distributed just-in-time building of shared libraries")
+ (description
+ "Dijitso provides a core component of the @code{FEniCS} framework,
+namely the just-in-time compilation of C++ code that is generated from
+Python modules. It is called from within a C++ library, using ctypes
+to import the dynamic shared library directly.
+
+As long as the compiled code can provide a simple factory function to
+a class implementing a predefined C++ interface, there is no limit to
+the complexity of that interface. Parallel support depends on the
+@code{mpi4py} interface.")
+ (license license:lgpl3+)))
+
+(define-public python-fenics-ufl
+ (package
+ (name "python-fenics-ufl")
+ (version "2018.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "fenics-ufl" version))
+ (sha256
+ (base32
+ "1fq8yc86s1s3c8c0b1rc2vf265q0hrkzg57100fg1nghcz0p4vla"))))
+ (build-system python-build-system)
+ (inputs
+ `(("python-numpy" ,python-numpy)))
+ (native-inputs
+ `(("python-pytest" ,python-pytest)))
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda _
+ (setenv "PYTHONPATH"
+ (string-append (getcwd) ":" (getenv "PYTHONPATH")))
+ (with-directory-excursion "test"
+ (invoke "py.test"))
+ #t)))))
+ (home-page "https://bitbucket.org/fenics-project/ufl/")
+ (synopsis "Unified language for form-compilers")
+ (description "The Unified Form Language (UFL) is a domain specific
+language for declaration of finite element discretizations of
+variational forms. More precisely, it defines a flexible interface
+for choosing finite element spaces and defining expressions for weak
+forms in a notation close to mathematical notation.
+
+UFL is part of the FEniCS Project.")
+ (license license:lgpl3+)))
+
+(define-public python-fenics-fiat
+ (package
+ (name "python-fenics-fiat")
+ (version "2018.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "fenics-fiat" version))
+ (sha256
+ (base32
+ "0fmjd93r6bwf6xs8csw86qzphrnr66xwv7f372w59gmq8mg6rljc"))))
+ (build-system python-build-system)
+ (native-inputs
+ `(("python-pytest" ,python-pytest)))
+ (propagated-inputs
+ `(("python-numpy" ,python-numpy)
+ ("python-sympy" ,python-sympy)))
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda _
+ (setenv "PYTHONPATH"
+ (string-append (getcwd) ":" (getenv "PYTHONPATH")))
+ (with-directory-excursion "test"
+ (invoke "py.test" "unit/"))
+ #t)))))
+ (home-page "https://bitbucket.org/fenics-project/fiat/")
+ (synopsis "Tabulation of finite element function spaces")
+ (description
+ "The FInite element Automatic Tabulator (FIAT) supports
+generation of arbitrary order instances of the Lagrange elements on
+lines, triangles, and tetrahedra. It is also capable of generating
+arbitrary order instances of Jacobi-type quadrature rules on the same
+element shapes. Further, H(div) and H(curl) conforming finite element
+spaces such as the families of Raviart-Thomas, Brezzi-Douglas-Marini
+and Nedelec are supported on triangles and tetrahedra. Upcoming
+versions will also support Hermite and nonconforming elements.
+
+FIAT is part of the FEniCS Project.")
+ (license license:lgpl3+)))
+
+(define-public python-fenics-ffc
+ (package
+ (name "python-fenics-ffc")
+ (version "2018.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "fenics-ffc" version))
+ (sha256
+ (base32
+ "1b2ia5vlkw298x7rf0k2p3ihlpwkwgc98p3s6sbpds3hqmfrzdz9"))))
+ (build-system python-build-system)
+ (native-inputs
+ `(("python-pytest" ,python-pytest)))
+ (propagated-inputs
+ `(("python-fenics-dijitso" ,python-fenics-dijitso)
+ ("python-fenics-fiat" ,python-fenics-fiat)
+ ("python-fenics-ufl" ,python-fenics-ufl)))
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda _
+ (setenv "HOME" (getcwd))
+ (setenv "PYTHONPATH"
+ (string-append (getcwd) ":" (getenv "PYTHONPATH")))
+ (with-directory-excursion "test"
+ ;; FIXME: the tests in subdirectory
+ ;; 'unit/ufc/finite_element' require the ffc_factory
+ ;; extension module. This module, located in the 'libs'
+ ;; subdirectory, needs to be built and made accessible
+ ;; prior to running the tests.
+ (invoke "py.test" "unit/" "--ignore=unit/ufc/")
+ (with-directory-excursion "uflacs"
+ (invoke "py.test" "unit/")))
+ #t)))))
+ (home-page "https://bitbucket.org/fenics-project/ffc/")
+ (synopsis "Compiler for finite element variational forms")
+ (description "The FEniCS Form Compiler (FFC) is a compiler for
+finite element variational forms. From a high-level description of
+the form, it generates efficient low-level C++ code that can be used
+to assemble the corresponding discrete operator (tensor). In
+particular, a bilinear form may be assembled into a matrix and a
+linear form may be assembled into a vector. FFC may be used either
+from the command line (by invoking the @code{ffc} command) or as a
+Python module (@code{import ffc}).
+
+FFC is part of the FEniCS Project.")
+ ;; There are two files released with a public domain licence;
+ ;; ufc.h and ufc_geometry.h, in subdirectory 'ffc/backends/ufc'.
+ (license (list license:public-domain license:lgpl3+))))
+
+(define-public fenics-dolfin
+ (package
+ (name "fenics-dolfin")
+ (version "2018.1.0.post1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://bitbucket.org/fenics-project/dolfin/get/"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "12zkk8j3xsg6l8p0ggwsl03084vlcivw4h99b7z9kndg7k89b3ya"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; Make sure we don't use the bundled test framework.
+ (delete-file-recursively "test/unit/cpp/catch")
+ (substitute* "test/unit/cpp/main.cpp"
+ ;; Use standard search paths for 'catch' header file.
+ (("#include.*")
+ "#include <catch.hpp>\n"))
+ (substitute* "test/unit/cpp/CMakeLists.txt"
+ ;; Add extra include directories required by the unit tests.
+ (("(^target_link_libraries.*)" line)
+ (string-append line "\n"
+ "target_include_directories("
+ "unittests PRIVATE "
+ "${DOLFIN_SOURCE_DIR} "
+ "${DOLFIN_SOURCE_DIR}/dolfin "
+ "${DOLFIN_BINARY_DIR})\n"))
+ (("(^set\\(CATCH_INCLUDE_DIR ).*(/catch\\))" _ front back)
+ (string-append front
+ "$ENV{CATCH_DIR}"
+ "/include" back "\n")))
+ (substitute* "demo/CMakeLists.txt"
+ ;; Add extra include directories required by the demo tests.
+ (("(^#find_package.*)" line)
+ (string-append line "\n"
+ "include_directories("
+ "${DOLFIN_SOURCE_DIR} "
+ "${DOLFIN_SOURCE_DIR}/dolfin "
+ "${DOLFIN_BINARY_DIR})\n")))
+ #t))))
+ (build-system cmake-build-system)
+ (inputs
+ `(("blas" ,openblas)
+ ("boost" ,boost)
+ ("eigen" ,eigen)
+ ("hdf5" ,hdf5-parallel-openmpi)
+ ("lapack" ,lapack)
+ ("libxml2" ,libxml2)
+ ("openmpi" ,openmpi)
+ ("python" ,python-3)
+ ("scotch" ,pt-scotch32)
+ ("suitesparse" ,suitesparse)
+ ("sundials" ,sundials-openmpi)
+ ("zlib" ,zlib)))
+ (native-inputs
+ `(("catch" ,catch-framework2)
+ ("pkg-config" ,pkg-config)))
+ (propagated-inputs
+ `(("ffc" ,python-fenics-ffc)
+ ("petsc" ,petsc-openmpi)
+ ("slepc" ,slepc-openmpi)))
+ (arguments
+ `(#:configure-flags
+ `("-DDOLFIN_ENABLE_DOCS:BOOL=OFF"
+ "-DDOLFIN_ENABLE_HDF5:BOOL=ON"
+ "-DDOLFIN_ENABLE_MPI:BOOL=ON"
+ "-DDOLFIN_ENABLE_PARMETIS:BOOL=OFF"
+ "-DDOLFIN_ENABLE_SCOTCH:BOOL=ON"
+ "-DDOLFIN_ENABLE_SUNDIALS:BOOL=ON"
+ "-DDOLFIN_ENABLE_TRILINOS:BOOL=OFF")
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'patch-usr-bin-file 'mpi-setup
+ ,%openmpi-setup)
+ (add-after 'patch-source-shebangs 'set-paths
+ (lambda _
+ ;; Define paths to store locations.
+ (setenv "BLAS_DIR" (assoc-ref %build-inputs "blas"))
+ (setenv "CATCH_DIR" (assoc-ref %build-inputs "catch"))
+ (setenv "LAPACK_DIR" (assoc-ref %build-inputs "lapack"))
+ (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
+ (setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc"))
+ (setenv "SCOTCH_DIR" (assoc-ref %build-inputs "scotch"))
+ (setenv "SUNDIALS_DIR" (assoc-ref %build-inputs "sundials"))
+ (setenv "UMFPACK_DIR" (assoc-ref %build-inputs "suitesparse"))
+ #t))
+ (add-before 'check 'pre-check
+ (lambda _
+ ;; The Dolfin repository uses git-lfs, whereby web links are
+ ;; substituted for large files. Guix does not currently support
+ ;; git-lfs, so only the links are downloaded. The tests that
+ ;; require the absent meshes cannot run and are skipped.
+ ;;
+ ;; Two other serial tests fail and are skipped.
+ ;; i) demo_stokes-iterative_serial,
+ ;; The MPI_Comm_rank() function was called before MPI_INIT was
+ ;; invoked
+ ;; ii) demo_multimesh-stokes_serial:
+ ;; Warning: Found no facets matching domain for boundary
+ ;; condition.
+ ;;
+ ;; One mpi test fails and is skipped.
+ ;; i) demo_stokes-iterative_mpi:
+ ;; The MPI_Comm_rank() function was called before MPI_INIT was
+ ;; invoked
+ (call-with-output-file "CTestCustom.cmake"
+ (lambda (port)
+ (display
+ (string-append
+ "set(CTEST_CUSTOM_TESTS_IGNORE "
+ "demo_bcs_serial "
+ "demo_bcs_mpi "
+ "demo_eigenvalue_serial "
+ "demo_eigenvalue_mpi "
+ "demo_navier-stokes_serial "
+ "demo_navier-stokes_mpi "
+ "demo_stokes-taylor-hood_serial "
+ "demo_stokes-taylor-hood_mpi "
+ "demo_subdomains_serial "
+ "demo_advection-diffusion_serial "
+ "demo_advection-diffusion_mpi "
+ "demo_auto-adaptive-navier-stokes_serial "
+ "demo_contact-vi-snes_serial "
+ "demo_contact-vi-snes_mpi "
+ "demo_contact-vi-tao_serial "
+ "demo_contact-vi-tao_mpi "
+ "demo_curl-curl_serial "
+ "demo_curl-curl_mpi "
+ "demo_dg-advection-diffusion_serial "
+ "demo_dg-advection-diffusion_mpi "
+ "demo_elasticity_serial "
+ "demo_elasticity_mpi "
+ "demo_elastodynamics_serial "
+ "demo_elastodynamics_mpi "
+ "demo_lift-drag_serial "
+ "demo_lift-drag_mpi "
+ "demo_mesh-quality_serial "
+ "demo_mesh-quality_mpi "
+ "demo_multimesh-stokes_serial "
+ "demo_stokes-iterative_serial "
+ "demo_stokes-iterative_mpi "
+ ")\n") port)))
+ #t))
+ (replace 'check
+ (lambda _
+ (and (invoke "make" "unittests")
+ (invoke "make" "demos")
+ (invoke "ctest" "-R" "unittests")
+ (invoke "ctest" "-R" "demo" "-R" "serial")
+ (invoke "ctest" "-R" "demo" "-R" "mpi")))))))
+ (home-page "https://bitbucket.org/fenics-project/dolfin/")
+ (synopsis "Problem solving environment for differential equations")
+ (description
+ "DOLFIN is a computational framework for finding numerical
+solutions to problems described by differential equations. Numerical
+models in DOLFIN are constructed using general families of finite
+elements. Data structures are provided for discretizing the governing
+system on a computational mesh. A compact syntax, similar to
+mathematical notation, is made available for defining function spaces
+and expressing variational forms. Interfaces to specialized matrix
+solvers are provided for solving the resultant linear systems.
+
+@code{fenics-dolfin} is part of the FEniCS project. It is the C++
+user interface to the FEniCS core components and external libraries.")
+ ;; The source code for the DOLFIN C++ library is licensed under the
+ ;; GNU Lesser General Public License, version 3 or later, with the
+ ;; following exceptions:
+ ;;
+ ;; public-domain: dolfin/geometry/predicates.cpp
+ ;; dolfin/geometry/predicates.h
+ ;;
+ ;; zlib: dolfin/io/base64.cpp
+ ;; dolfin/io/base64.h
+ ;;
+ ;; expat: dolfin/io/pugiconfig.hpp
+ ;; dolfin/io/pugixml.cpp
+ ;; dolfin/io/pugixml.hpp
+ (license (list license:public-domain
+ license:zlib
+ license:expat
+ license:lgpl3+))))
+
+(define-public fenics
+ (package (inherit fenics-dolfin)
+ (name "fenics")
+ (build-system python-build-system)
+ (inputs
+ `(("pybind11" ,pybind11)
+ ("python-matplotlib" ,python-matplotlib)
+ ,@(alist-delete "python" (package-inputs fenics-dolfin))))
+ (native-inputs
+ `(("cmake" ,cmake)
+ ("ply" ,python-ply)
+ ("pytest" ,python-pytest)
+ ("python-decorator" ,python-decorator)
+ ("python-pkgconfig" ,python-pkgconfig)
+ ,@(package-native-inputs fenics-dolfin)))
+ (propagated-inputs
+ `(("dolfin" ,fenics-dolfin)
+ ("petsc4py" ,python-petsc4py)
+ ("slepc4py" ,python-slepc4py)))
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'patch-source-shebangs 'set-paths
+ (lambda _
+ ;; Define paths to store locations.
+ (setenv "PYBIND11_DIR" (assoc-ref %build-inputs "pybind11"))
+ ;; Move to python sub-directory.
+ (chdir "python")
+ #t))
+ (add-after 'build 'mpi-setup
+ ,%openmpi-setup)
+ (add-before 'check 'pre-check
+ (lambda _
+ ;; Exclude tests that require meshes supplied by git-lfs.
+ (substitute* "demo/test.py"
+ (("(.*stem !.*)" line)
+ (string-append
+ line "\n"
+ "excludeList = [\n"
+ "'multimesh-quadrature', \n"
+ "'multimesh-marking', \n"
+ "'mixed-poisson-sphere', \n"
+ "'mesh-quality', \n"
+ "'lift-drag', \n"
+ "'elastodynamics', \n"
+ "'dg-advection-diffusion', \n"
+ "'contact-vi-tao', \n"
+ "'contact-vi-snes', \n"
+ "'collision-detection', \n"
+ "'buckling-tao', \n"
+ "'auto-adaptive-navier-stokes', \n"
+ "'advection-diffusion', \n"
+ "'subdomains', \n"
+ "'stokes-taylor-hood', \n"
+ "'stokes-mini', \n"
+ "'navier-stokes', \n"
+ "'eigenvalue']\n"
+ "demos = ["
+ "d for d in demos if d[0].stem not in "
+ "excludeList]\n")))
+ (setenv "HOME" (getcwd))
+ (setenv "PYTHONPATH"
+ (string-append
+ (getcwd) "/build/lib.linux-x86_64-"
+ ,(version-major+minor (package-version python)) ":"
+ (getenv "PYTHONPATH")))
+ ;; Restrict OpenBLAS to MPI-only in preference to MPI+OpenMP.
+ (setenv "OPENBLAS_NUM_THREADS" "1")
+ #t))
+ (replace 'check
+ (lambda _
+ (with-directory-excursion "test"
+ ;; Note: The test test_snes_set_from_options() in the file
+ ;; unit/nls/test_PETScSNES_solver.py fails and is ignored.
+ (and (invoke "py.test" "unit" "--ignore"
+ "unit/nls/test_PETScSNES_solver.py")
+ (invoke "mpirun" "-np" "3" "python" "-B" "-m"
+ "pytest" "unit" "--ignore"
+ "unit/nls/test_PETScSNES_solver.py")))
+ (with-directory-excursion "demo"
+ ;; Check demos.
+ (invoke "python" "generate-demo-files.py")
+ (and (invoke "python" "-m" "pytest" "-v" "test.py")
+ (invoke "python" "-m" "pytest" "-v" "test.py"
+ "--mpiexec=mpiexec" "--num-proc=3")))
+ #t))
+ (add-after 'install 'install-demo-files
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((demos (string-append
+ (assoc-ref outputs "out")
+ "/share/python-dolfin/demo")))
+ (mkdir-p demos)
+ (with-directory-excursion "demo"
+ (for-each (lambda (file)
+ (let* ((dir (dirname file))
+ (tgt-dir (string-append demos "/" dir)))
+ (unless (equal? "." dir)
+ (mkdir-p tgt-dir)
+ (install-file file tgt-dir))))
+ (find-files "." ".*\\.(py|gz|xdmf)$"))))
+ #t)))))
+ (home-page "https://fenicsproject.org/")
+ (synopsis "High-level environment for solving differential equations")
+ (description
+ "@code{fenics} is a computing platform for solving general classes of
+problems that involve differential equations. @code{fenics} facilitates
+access to efficient methods for dealing with ordinary differential
+equations (ODEs) and partial differential equations (PDEs). Systems of
+equations such as these are commonly encountered in areas of engineering,
+mathematics and the physical sciences. It is particularly well-suited to
+problems that can be solved using the Finite Element Method (FEM).
+
+@code{fenics} is the top level of the set of packages that are developed
+within the FEniCS project. It provides the python user interface to the
+FEniCS core components and external libraries.")
+ (license license:lgpl3+)))
generated by cgit v1.2.3 (git 2.45.2) at 2024-08-10 09:50:49 +0000